TOMTOM

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

Query Motifs | Target Databases | Matches | Program information | Explanation

Query Motifs

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Name	Alt. Name	Preview	Matches	List
ADCCRG	2.3e-1045	AGCCAG	1	MA0145.1 (Tcfcp2l1)
ARCWGGW	3.6e-263	AGCAGGA	0
CNGGAA	4.2e-125	CTGGAA	1	MA0144.1 (Stat3)
CMCRCCC	1.6e-102	CCCACCC	6	MA0039.2 (Klf4) , Klf7_primary, Sox13_secondary, Ascl2_secondary, MA0162.1 (Egr1) , Sp4_primary
AAGGTCA	7.3e-097	AAGGTCA	10	MA0141.1 (Esrrb) , MA0115.1 (NR1H2::RXRA) , MA0065.1 (PPARG::RXRA) , Rara_primary, Esrra_primary, Nr2f2_primary, MA0160.1 (NR4A2) , MA0071.1 (RORA_1) , MA0017.1 (NR2F1) , MA0065.2 (PPARG::RXRA)
CCAGHY	1.3e-057	CCAGCC	0
RGGCGGW	2.3e-047	GGGCGGA	1	Egr1_primary
ACAAWGV	2.6e-046	ACAAAGG	5	Sox11_primary, Sox4_primary, Sox12_secondary, MA0442.1 (SOX10) , MA0143.1 (Sox2)
ADCCTGY	6.0e-042	AGCCTGC	0
ATKYAAA	9.4e-028	ATGCAAA	3	Pou2f2_3748.1, MA0142.1 (Pou5f1) , Pou2f3_3986.2
AGGCRG	7.1e-026	AGGCAG	0
CTAGTTH	4.6e-025	CTAGTTT	0
CCGGTMH	1.3e-024	CCGGTCC	1	MA0076.1 (ELK4)
AAACAAD	9.4e-019	AAACAAG	3	MA0157.1 (FOXO3) , Foxk1_primary, MA0030.1 (FOXF2)
CACGTGD	2.5e-016	CACGTGG	10	MA0093.1 (USF1) , MA0058.1 (MAX) , MA0104.1 (Mycn) , MA0004.1 (Arnt) , Max_primary, MA0059.1 (MYC::MAX) , MA0104.2 (Mycn) , MA0147.1 (Myc) , Bhlhb2_secondary, Bhlhb2_primary
DATAAA	2.0e-014	AATAAA	0
AYACAG	3.0e-010	ACACAG	0
AGGTYAC	1.3e-010	AGGTCAC	7	MA0160.1 (NR4A2) , MA0141.1 (Esrrb) , Rara_primary, MA0071.1 (RORA_1) , MA0112.1 (ESR1) , MA0112.2 (ESR1) , MA0066.1 (PPARG)
GGGAGGR	3.5e-010	GGGAGGG	1	MA0079.2 (SP1)
WTTCTR	7.9e-008	TTTCTG	0
AGGDCAG	3.7e-008	AGGGCAG	0
CMGCCGC	3.3e-007	CCGCCGC	0
ACATTYC	1.7e-005	ACATTCC	1	MA0090.1 (TEAD1)
AGAMCAG	3.9e-005	AGAACAG	1	MA0091.1 (TAL1::TCF3)
CCGGM	6.5e-004	CCGGC	0
AAAGCAG	9.3e-004	AAAGCAG	0
ATTAGCA	2.9e-003	ATTAGCA	0
ATAAWTA	3.3e-003	ATAATTA	0
KCTGGGA	7.1e-003	GCTGGGA	0
GASGTCA	6.4e-003	GAGGTCA	2	MA0159.1 (RXR::RAR_DR5) , MA0018.2 (CREB1)
AGGAMA	9.1e-003	AGGAAA	0
ATCCTG	9.1e-003	ATCCTG	0

Target Databases

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Database	Number of Motifs	Motifs Matched
jaspar_vertebrates.meme	146	32
uniprobe_mouse.meme	386	17

Matches to Query: ADCCRG (2.3e-1045)

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Summary

Alignment

Name	MA0145.1
Alt. Name	Tcfcp2l1
Database	jaspar_vertebrates.meme
p-value	1.05474e-05
E-value	0.00561121
q-value	0.0112224
Overlap	6
Offset	8
Orientation	Normal

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Matches to Query: ARCWGGW (3.6e-263)

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Matches to Query: CNGGAA (4.2e-125)

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Summary

Alignment

Name	MA0144.1
Alt. Name	Stat3
Database	jaspar_vertebrates.meme
p-value	3.53115e-05
E-value	0.0187857
q-value	0.0185962
Overlap	6
Offset	4
Orientation	Reverse Complement

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Matches to Query: CMCRCCC (1.6e-102)

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Summary

Alignment

Name	MA0039.2
Alt. Name	Klf4
Database	jaspar_vertebrates.meme
p-value	7.23733e-10
E-value	3.85026e-07
q-value	7.57919e-07
Overlap	7
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	Klf7_primary
Database	uniprobe_mouse.meme
p-value	1.87292e-06
E-value	0.000996393
q-value	0.000980694
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Sox13_secondary
Database	uniprobe_mouse.meme
p-value	5.4307e-06
E-value	0.00288913
q-value	0.00189574
Overlap	7
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	Ascl2_secondary
Database	uniprobe_mouse.meme
p-value	2.69001e-05
E-value	0.0143108
q-value	0.00704268
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0162.1
Alt. Name	Egr1
Database	jaspar_vertebrates.meme
p-value	4.58578e-05
E-value	0.0243963
q-value	0.00960478
Overlap	6
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	Sp4_primary
Database	uniprobe_mouse.meme
p-value	9.37108e-05
E-value	0.0498541
q-value	0.0152588
Overlap	7
Offset	3
Orientation	Normal

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Matches to Query: AAGGTCA (7.3e-097)

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Summary

Alignment

Name	MA0141.1
Alt. Name	Esrrb
Database	jaspar_vertebrates.meme
p-value	1.60179e-07
E-value	8.52154e-05
q-value	0.000100647
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0115.1
Alt. Name	NR1H2::RXRA
Database	jaspar_vertebrates.meme
p-value	2.40269e-07
E-value	0.000127823
q-value	0.000100647
Overlap	7
Offset	8
Orientation	Normal

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Summary

Alignment

Name	MA0065.1
Alt. Name	PPARG::RXRA
Database	jaspar_vertebrates.meme
p-value	2.88323e-07
E-value	0.000153388
q-value	0.000100647
Overlap	7
Offset	10
Orientation	Normal

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Summary

Alignment

Name	Rara_primary
Database	uniprobe_mouse.meme
p-value	1.73894e-06
E-value	0.000925114
q-value	0.000390231
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Esrra_primary
Database	uniprobe_mouse.meme
p-value	1.86315e-06
E-value	0.000991193
q-value	0.000390231
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Nr2f2_primary
Database	uniprobe_mouse.meme
p-value	3.13431e-06
E-value	0.00166745
q-value	0.00054706
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0160.1
Alt. Name	NR4A2
Database	jaspar_vertebrates.meme
p-value	6.93074e-06
E-value	0.00368715
q-value	0.00103687
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0071.1
Alt. Name	RORA_1
Database	jaspar_vertebrates.meme
p-value	1.95905e-05
E-value	0.0104222
q-value	0.00256449
Overlap	7
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0017.1
Alt. Name	NR2F1
Database	jaspar_vertebrates.meme
p-value	5.60188e-05
E-value	0.029802
q-value	0.00651833
Overlap	7
Offset	7
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0065.2
Alt. Name	PPARG::RXRA
Database	jaspar_vertebrates.meme
p-value	8.81085e-05
E-value	0.0468737
q-value	0.00922704
Overlap	7
Offset	8
Orientation	Normal

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Matches to Query: CCAGHY (1.3e-057)

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Matches to Query: RGGCGGW (2.3e-047)

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Summary

Alignment

Name	Egr1_primary
Database	uniprobe_mouse.meme
p-value	3.72454e-05
E-value	0.0198146
q-value	0.0391077
Overlap	7
Offset	7
Orientation	Reverse Complement

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Matches to Query: ACAAWGV (2.6e-046)

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Summary

Alignment

Name	Sox11_primary
Database	uniprobe_mouse.meme
p-value	2.76412e-07
E-value	0.000147051
q-value	0.000290024
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	Sox4_primary
Database	uniprobe_mouse.meme
p-value	8.65761e-07
E-value	0.000460585
q-value	0.000454198
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	Sox12_secondary
Database	uniprobe_mouse.meme
p-value	2.84318e-06
E-value	0.00151257
q-value	0.000994399
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MA0442.1
Alt. Name	SOX10
Database	jaspar_vertebrates.meme
p-value	5.74505e-06
E-value	0.00305637
q-value	0.00150699
Overlap	6
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0143.1
Alt. Name	Sox2
Database	jaspar_vertebrates.meme
p-value	1.5588e-05
E-value	0.00829279
q-value	0.00327112
Overlap	7
Offset	8
Orientation	Reverse Complement

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Matches to Query: ADCCTGY (6.0e-042)

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Matches to Query: ATKYAAA (9.4e-028)

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Summary

Alignment

Name	Pou2f2_3748.1
Database	uniprobe_mouse.meme
p-value	1.93986e-05
E-value	0.01032
q-value	0.00969457
Overlap	7
Offset	4
Orientation	Normal

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Summary

Alignment

Name	MA0142.1
Alt. Name	Pou5f1
Database	jaspar_vertebrates.meme
p-value	2.1456e-05
E-value	0.0114146
q-value	0.00969457
Overlap	7
Offset	7
Orientation	Normal

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Summary

Alignment

Name	Pou2f3_3986.2
Database	uniprobe_mouse.meme
p-value	2.73519e-05
E-value	0.0145512
q-value	0.00969457
Overlap	7
Offset	4
Orientation	Normal

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Matches to Query: AGGCRG (7.1e-026)

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Matches to Query: CTAGTTH (4.6e-025)

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Matches to Query: CCGGTMH (1.3e-024)

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Summary

Alignment

Name	MA0076.1
Alt. Name	ELK4
Database	jaspar_vertebrates.meme
p-value	1.8473e-05
E-value	0.00982766
q-value	0.0196553
Overlap	5
Offset	4
Orientation	Reverse Complement

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Matches to Query: AAACAAD (9.4e-019)

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Summary

Alignment

Name	MA0157.1
Alt. Name	FOXO3
Database	jaspar_vertebrates.meme
p-value	3.92483e-05
E-value	0.0208801
q-value	0.0221762
Overlap	5
Offset	3
Orientation	Normal

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Summary

Alignment

Name	Foxk1_primary
Database	uniprobe_mouse.meme
p-value	6.47304e-05
E-value	0.0344366
q-value	0.0221762
Overlap	7
Offset	7
Orientation	Normal

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Summary

Alignment

Name	MA0030.1
Alt. Name	FOXF2
Database	jaspar_vertebrates.meme
p-value	8.23654e-05
E-value	0.0438184
q-value	0.0221762
Overlap	7
Offset	7
Orientation	Normal

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Matches to Query: CACGTGD (2.5e-016)

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Summary

Alignment

Name	MA0093.1
Alt. Name	USF1
Database	jaspar_vertebrates.meme
p-value	1.09367e-08
E-value	5.81835e-06
q-value	9.1451e-06
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0058.1
Alt. Name	MAX
Database	jaspar_vertebrates.meme
p-value	1.74988e-08
E-value	9.30936e-06
q-value	9.1451e-06
Overlap	7
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0104.1
Alt. Name	Mycn
Database	jaspar_vertebrates.meme
p-value	1.03393e-06
E-value	0.000550048
q-value	0.000180114
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0004.1
Alt. Name	Arnt
Database	jaspar_vertebrates.meme
p-value	2.65571e-06
E-value	0.00141284
q-value	0.000346977
Overlap	6
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Max_primary
Database	uniprobe_mouse.meme
p-value	4.02961e-06
E-value	0.00214375
q-value	0.000467984
Overlap	7
Offset	4
Orientation	Normal

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Summary

Alignment

Name	MA0059.1
Alt. Name	MYC::MAX
Database	jaspar_vertebrates.meme
p-value	1.22092e-05
E-value	0.00649532
q-value	0.00127614
Overlap	7
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0104.2
Alt. Name	Mycn
Database	jaspar_vertebrates.meme
p-value	1.3502e-05
E-value	0.00718306
q-value	0.00128297
Overlap	7
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MA0147.1
Alt. Name	Myc
Database	jaspar_vertebrates.meme
p-value	1.66113e-05
E-value	0.00883719
q-value	0.00141531
Overlap	7
Offset	2
Orientation	Normal

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Summary

Alignment

Name	Bhlhb2_secondary
Database	uniprobe_mouse.meme
p-value	1.7603e-05
E-value	0.00936477
q-value	0.00141531
Overlap	7
Offset	8
Orientation	Normal

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Summary

Alignment

Name	Bhlhb2_primary
Database	uniprobe_mouse.meme
p-value	8.77608e-05
E-value	0.0466887
q-value	0.00482789
Overlap	7
Offset	8
Orientation	Reverse Complement

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Matches to Query: DATAAA (2.0e-014)

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Matches to Query: AYACAG (3.0e-010)

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Matches to Query: AGGTYAC (1.3e-010)

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Summary

Alignment

Name	MA0160.1
Alt. Name	NR4A2
Database	jaspar_vertebrates.meme
p-value	8.15371e-06
E-value	0.00433778
q-value	0.00597905
Overlap	7
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0141.1
Alt. Name	Esrrb
Database	jaspar_vertebrates.meme
p-value	1.6259e-05
E-value	0.00864977
q-value	0.00597905
Overlap	6
Offset	6
Orientation	Normal

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Summary

Alignment

Name	Rara_primary
Database	uniprobe_mouse.meme
p-value	1.71117e-05
E-value	0.00910341
q-value	0.00597905
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MA0071.1
Alt. Name	RORA_1
Database	jaspar_vertebrates.meme
p-value	2.73642e-05
E-value	0.0145578
q-value	0.00678241
Overlap	6
Offset	4
Orientation	Normal

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Summary

Alignment

Name	MA0112.1
Alt. Name	ESR1
Database	jaspar_vertebrates.meme
p-value	3.23514e-05
E-value	0.0172109
q-value	0.00678241
Overlap	7
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MA0112.2
Alt. Name	ESR1
Database	jaspar_vertebrates.meme
p-value	5.24242e-05
E-value	0.0278897
q-value	0.00915886
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0066.1
Alt. Name	PPARG
Database	jaspar_vertebrates.meme
p-value	6.23495e-05
E-value	0.0331699
q-value	0.00933675
Overlap	7
Offset	2
Orientation	Normal

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Matches to Query: GGGAGGR (3.5e-010)

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Summary

Alignment

Name	MA0079.2
Alt. Name	SP1
Database	jaspar_vertebrates.meme
p-value	5.02034e-05
E-value	0.0267082
q-value	0.0526882
Overlap	7
Offset	2
Orientation	Reverse Complement

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Matches to Query: WTTCTR (7.9e-008)

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Matches to Query: AGGDCAG (3.7e-008)

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Matches to Query: CMGCCGC (3.3e-007)

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Matches to Query: ACATTYC (1.7e-005)

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Summary

Alignment

Name	MA0090.1
Alt. Name	TEAD1
Database	jaspar_vertebrates.meme
p-value	1.62454e-05
E-value	0.00864253
q-value	0.0172851
Overlap	7
Offset	1
Orientation	Normal

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Matches to Query: AGAMCAG (3.9e-005)

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Summary

Alignment

Name	MA0091.1
Alt. Name	TAL1::TCF3
Database	jaspar_vertebrates.meme
p-value	2.99529e-05
E-value	0.015935
q-value	0.0318699
Overlap	5
Offset	-2
Orientation	Reverse Complement

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Matches to Query: CCGGM (6.5e-004)

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Matches to Query: AAAGCAG (9.3e-004)

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Matches to Query: ATTAGCA (2.9e-003)

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Matches to Query: ATAAWTA (3.3e-003)

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Matches to Query: KCTGGGA (7.1e-003)

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Matches to Query: GASGTCA (6.4e-003)

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Summary

Alignment

Name	MA0159.1
Alt. Name	RXR::RAR_DR5
Database	jaspar_vertebrates.meme
p-value	5.43027e-05
E-value	0.028889
q-value	0.0441603
Overlap	7
Offset	10
Orientation	Normal

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Summary

Alignment

Name	MA0018.2
Alt. Name	CREB1
Database	jaspar_vertebrates.meme
p-value	9.38007e-05
E-value	0.049902
q-value	0.0441603
Overlap	7
Offset	1
Orientation	Normal

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Matches to Query: AGGAMA (9.1e-003)

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Matches to Query: ATCCTG (9.1e-003)

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TOMTOM version

4.5.0 (Release date: Wed Oct 20 15:18:53 EST 2010)

Reference

Shobhit Gupta, John A. Stamatoyannopoulos, Timothy L. Bailey and William Stafford Noble, "Quantifying similarity between motifs",
Genome Biology, 8:R24, 2007

Command line summary

tomtom -oc CHEN_RESULTS.13.10.10/Tcfcp2l1.tomtom -min-overlap 5 -dist pearson -evalue -thresh 0.05 -no-ssc CHEN_RESULTS.13.10.10/Tcfcp2l1.dreme motif_databases/jaspar_vertebrates.meme motif_databases/uniprobe_mouse.meme

Background letter frequencies (from first motif database):

A: 0.250 C: 0.250 G: 0.250 T: 0.250

Result calculation took 14.179 seconds

show model parameters...

Model parameters

distance_measure      = value: "pearson"
threshold             = type: "evalue"
background            = from: "first_target", A: "0.25", C: "0.25", G: "0.25", T: "0.25"
host                  = tlb-kamikaze-lt.imb.uq.edu.au
when                  = Fri Nov 19 15:50:47 2010

Explanation of TOMTOM Results

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The TOMTOM results consist of

The query motifs with links to further information on matches. [View]
The target databases with information on the number of matches. [View]
The matches between query motifs and target motifs. [View]
- The summary of match information.
- An alignment of the two motifs.
The program details including:
1. The version of TOMTOM and the date it was released. [View]
2. The reference to cite if you use TOMTOM in your research. [View]
3. The command line summary detailing the parameters with which you ran TOMTOM. [View]
This explanation of how to interpret TOMTOM results.

Inputs

The important inputs to TOMTOM.

Query Motifs

The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name: The motif name.
Alt. Name: The alternative motif name. This column may be hidden if no query motifs have an alternate name.
Website: A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.
Preview: The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.
Matches: The number of significant matches.
List: Links to the first 20 matches

Target Databases

The target motifs section lists details on the motif databases that were specifed to search.

Database: The database name.
Number of Motifs: The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.
Motifs Matched: The number of motifs that had a match with at least one of the query motifs.

Matches

The matches section list the group of motifs that match each query motif. For each query-target match the following information is given:

Summary Table

The summary gives the important statistics about the motif match.

Name: The name of the matched motif.
Alt. Name: The alternative name of the matched motif.
p-value: The probability that the match occurred by random chance according to the null model.
E-value: The expected number of false positives in the matches up to this point.
q-value: The minimum False Discovery Rate required to include the match.
Overlap: The number of letters that overlaped in the optimal alignment.
Offset: The offset of the query motif to the matched motif in the optimal alignment.
Orientation: The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.

Alignment

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

Create custom LOGO

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type: Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.
Error bars: Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.
SSC: Toggle adding pseudocounts for Small Sample Correction.
Flip: Toggle a full reverse complement of the alignment.
Width: Specify the width of the generated motif.
Height: Specify the height of the generated motif.

Query Motifs

Name

Alt. Name

Preview

Matches

List

Target Databases

Database

Number of Motifs

Motifs Matched

Matches to Query: ADCCRG (2.3e-1045)

Summary

Alignment

Matches to Query: ARCWGGW (3.6e-263)

Matches to Query: CNGGAA (4.2e-125)

Summary

Alignment

Matches to Query: CMCRCCC (1.6e-102)

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: AAGGTCA (7.3e-097)

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: CCAGHY (1.3e-057)

Matches to Query: RGGCGGW (2.3e-047)

Summary

Alignment

Matches to Query: ACAAWGV (2.6e-046)

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: ADCCTGY (6.0e-042)

Matches to Query: ATKYAAA (9.4e-028)

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: AGGCRG (7.1e-026)

Matches to Query: CTAGTTH (4.6e-025)

Matches to Query: CCGGTMH (1.3e-024)

Summary

Alignment

Matches to Query: AAACAAD (9.4e-019)